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- PDB-5ick: A unique binding model of FXR LBD with feroline -

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Basic information

Entry
Database: PDB / ID: 5ick
TitleA unique binding model of FXR LBD with feroline
Components
  • Bile acid receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Complex
Function / homology
Function and homology information


regulation of urea metabolic process / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production ...regulation of urea metabolic process / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of monocyte chemotactic protein-1 production / toll-like receptor 9 signaling pathway / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / bile acid metabolic process / bile acid binding / cell-cell junction assembly / cellular response to fatty acid / regulation of cholesterol metabolic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / negative regulation of interleukin-2 production / bile acid and bile salt transport / intracellular glucose homeostasis / locomotor rhythm / positive regulation of interleukin-17 production / aryl hydrocarbon receptor binding / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of insulin receptor signaling pathway / fatty acid homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / nuclear retinoid X receptor binding / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / intracellular receptor signaling pathway / positive regulation of adipose tissue development / : / Notch signaling pathway / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / response to progesterone / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / negative regulation of smoothened signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / euchromatin / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / : / HATs acetylate histones / cellular response to lipopolysaccharide / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / receptor complex / transcription cis-regulatory region binding / protein dimerization activity / nuclear speck / defense response to bacterium / nuclear body / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / innate immune response
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FEZ / Nuclear receptor coactivator 2 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.47 Å
AuthorsLu, Y. / Li, Y.
CitationJournal: Chembiochem / Year: 2017
Title: A Novel Class of Natural FXR Modulators with a Unique Mode of Selective Co-regulator Assembly
Authors: Zheng, W. / Lu, Y. / Lin, S. / Wang, R. / Qiu, L. / Zhu, Y. / Yao, B. / Guo, F. / Jin, S. / Jin, L. / Li, Y.
History
DepositionFeb 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile acid receptor
B: Bile acid receptor
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3527
Polymers56,2774
Non-polymers1,0753
Water1,09961
1
A: Bile acid receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4973
Polymers28,1382
Non-polymers3581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-5 kcal/mol
Surface area11840 Å2
MethodPISA
2
B: Bile acid receptor
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8554
Polymers28,1382
Non-polymers7172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.161, 34.910, 134.915
Angle α, β, γ (deg.)90.000, 90.510, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Bile acid receptor


Mass: 26802.789 Da / Num. of mol.: 2 / Fragment: UNP residues 258-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RI1
#2: Protein/peptide Nuclear receptor coactivator 2


Mass: 1335.550 Da / Num. of mol.: 2 / Fragment: UNP residues 742-752
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15596
#3: Chemical ChemComp-FEZ / (1S,2S,3Z,5S,8Z)-5-hydroxy-5,9-dimethyl-2-(propan-2-yl)cyclodeca-3,8-dien-1-yl 4-hydroxybenzoate / FEROLINE


Mass: 358.471 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H30O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3350 and 0.2 M ammonia acetate

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.47→134.91 Å / Num. obs: 19055

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
Cootmodel building
RefinementResolution: 2.47→50.01 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.805 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 938 4.9 %RANDOM
Rwork0.2123 ---
obs0.2155 18127 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.33 Å2 / Biso mean: 40.897 Å2 / Biso min: 15.52 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å2-0 Å21.47 Å2
2---2.35 Å20 Å2
3----1.77 Å2
Refinement stepCycle: final / Resolution: 2.47→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 78 61 4079
Biso mean--38.78 36.25 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194101
X-RAY DIFFRACTIONr_bond_other_d00.023990
X-RAY DIFFRACTIONr_angle_refined_deg2.041.9925541
X-RAY DIFFRACTIONr_angle_other_deg3.59939200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0535475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8525.025201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.44915767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3331520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214512
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02924
X-RAY DIFFRACTIONr_mcbond_it2.9733.8311912
X-RAY DIFFRACTIONr_mcbond_other2.9723.8311913
X-RAY DIFFRACTIONr_mcangle_it4.7095.7342383
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 66 -
Rwork0.224 1330 -
all-1396 -
obs--99.29 %

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